fix: bd repo commands write to YAML and cleanup on remove (#683)

- bd repo add/remove now writes to .beads/config.yaml instead of database
- bd repo remove deletes hydrated issues from the removed repo
- Added internal/config/repos.go for YAML config manipulation
- Added DeleteIssuesBySourceRepo for cleanup on remove

Fixes config disconnect where bd repo add wrote to DB but hydration read from YAML.

Breaking change: bd repo add no longer accepts optional alias argument.

Co-authored-by: Dylan Conlin <dylan.conlin@gmail.com>

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

cmd/bd/repo.go

@@ -1,119 +1,157 @@
 package main
 
 import (
-	"context"
 	"encoding/json"
 	"fmt"
 	"os"
-	"strings"
+	"path/filepath"
 
 	"github.com/spf13/cobra"
-	"github.com/steveyegge/beads/internal/storage"
+	"github.com/steveyegge/beads/internal/config"
+	"github.com/steveyegge/beads/internal/storage/sqlite"
 )
 
 var repoCmd = &cobra.Command{
 	Use:     "repo",
 	GroupID: "advanced",
 	Short:   "Manage multiple repository configuration",
-	Long: `Configure and manage multiple repository support for multi-clone sync.
+	Long: `Configure and manage multiple repository support for multi-repo hydration.
+
+Multi-repo support allows hydrating issues from multiple beads repositories
+into a single database for unified cross-repo issue tracking.
+
+Configuration is stored in .beads/config.yaml under the 'repos' section:
+
+  repos:
+    primary: "."
+    additional:
+      - ~/beads-planning
+      - ~/work-repo
 
 Examples:
-  bd repo add ~/.beads-planning      # Add planning repo
-  bd repo add ../other-repo "notes"  # Add with alias
+  bd repo add ~/beads-planning       # Add planning repo
+  bd repo add ../other-repo          # Add relative path repo
   bd repo list                       # Show all configured repos
-  bd repo remove notes               # Remove by alias
-  bd repo remove ~/.beads-planning   # Remove by path`,
+  bd repo remove ~/beads-planning    # Remove by path
+  bd repo sync                       # Sync from all configured repos`,
 }
 
 var repoAddCmd = &cobra.Command{
-	Use:   "add <path> [alias]",
+	Use:   "add <path>",
 	Short: "Add an additional repository to sync",
-	Args:  cobra.RangeArgs(1, 2),
+	Long: `Add a repository path to the repos.additional list in config.yaml.
+
+The path should point to a directory containing a .beads folder.
+Paths can be absolute or relative (they are stored as-is).
+
+This modifies .beads/config.yaml, which is version-controlled and
+shared across all clones of this repository.`,
+	Args: cobra.ExactArgs(1),
 	RunE: func(cmd *cobra.Command, args []string) error {
-		if err := ensureDirectMode("repo add requires direct database access"); err != nil {
-			return err
+		repoPath := args[0]
+
+		// Expand ~ to home directory for validation and display
+		expandedPath := repoPath
+		if len(repoPath) > 0 && repoPath[0] == '~' {
+			home, err := os.UserHomeDir()
+			if err == nil {
+				expandedPath = filepath.Join(home, repoPath[1:])
+			}
 		}
 
-		ctx := rootCtx
-		path := args[0]
-		var alias string
-		if len(args) > 1 {
-			alias = args[1]
+		// Validate the repo path exists and has .beads
+		beadsDir := filepath.Join(expandedPath, ".beads")
+		if _, err := os.Stat(beadsDir); os.IsNotExist(err) {
+			return fmt.Errorf("no .beads directory found at %s - is this a beads repository?", expandedPath)
 		}
 
-		// Use path as key if no alias provided
-		key := alias
-		if key == "" {
-			key = path
-		}
-
-		// Get existing repos
-		existing, err := getRepoConfig(ctx, store)
+		// Find config.yaml
+		configPath, err := config.FindConfigYAMLPath()
 		if err != nil {
-			return fmt.Errorf("failed to get existing repos: %w", err)
+			return fmt.Errorf("failed to find config.yaml: %w", err)
 		}
 
-		existing[key] = path
-
-		// Save back
-		if err := setRepoConfig(ctx, store, existing); err != nil {
-			return fmt.Errorf("failed to save config: %w", err)
+		// Add the repo (use original path to preserve ~ etc.)
+		if err := config.AddRepo(configPath, repoPath); err != nil {
+			return fmt.Errorf("failed to add repository: %w", err)
 		}
 
 		if jsonOutput {
 			result := map[string]interface{}{
 				"added": true,
-				"key":   key,
-				"path":  path,
+				"path":  repoPath,
 			}
 			return json.NewEncoder(os.Stdout).Encode(result)
 		}
 
-		fmt.Printf("Added repository: %s → %s\n", key, path)
+		fmt.Printf("Added repository: %s\n", repoPath)
+		fmt.Printf("Run 'bd repo sync' to hydrate issues from this repository.\n")
 		return nil
 	},
 }
 
 var repoRemoveCmd = &cobra.Command{
-	Use:   "remove <key>",
+	Use:   "remove <path>",
 	Short: "Remove a repository from sync configuration",
-	Args:  cobra.ExactArgs(1),
+	Long: `Remove a repository path from the repos.additional list in config.yaml.
+
+The path must exactly match what was added (e.g., if you added "~/foo",
+you must remove "~/foo", not "/home/user/foo").
+
+This command also removes any previously-hydrated issues from the database
+that came from the removed repository.`,
+	Args: cobra.ExactArgs(1),
 	RunE: func(cmd *cobra.Command, args []string) error {
+		repoPath := args[0]
+
+		// Ensure we have direct database access for cleanup
 		if err := ensureDirectMode("repo remove requires direct database access"); err != nil {
 			return err
 		}
 
 		ctx := rootCtx
-		key := args[0]
 
-		// Get existing repos
-		existing, err := getRepoConfig(ctx, store)
+		// Delete issues from the removed repo before removing from config
+		// The source_repo field uses the original path (e.g., "~/foo")
+		deletedCount := 0
+		if sqliteStore, ok := store.(*sqlite.SQLiteStorage); ok {
+			count, err := sqliteStore.DeleteIssuesBySourceRepo(ctx, repoPath)
+			if err != nil {
+				return fmt.Errorf("failed to delete issues from repo: %w", err)
+			}
+			deletedCount = count
+
+			// Also clear the mtime cache entry
+			if err := sqliteStore.ClearRepoMtime(ctx, repoPath); err != nil {
+				// Non-fatal: just log a warning
+				fmt.Fprintf(os.Stderr, "Warning: failed to clear mtime cache: %v\n", err)
+			}
+		}
+
+		// Find config.yaml
+		configPath, err := config.FindConfigYAMLPath()
 		if err != nil {
-			return fmt.Errorf("failed to get existing repos: %w", err)
+			return fmt.Errorf("failed to find config.yaml: %w", err)
 		}
 
-		path, exists := existing[key]
-		if !exists {
-			return fmt.Errorf("repository not found: %s", key)
-		}
-
-		delete(existing, key)
-
-		// Save back
-		if err := setRepoConfig(ctx, store, existing); err != nil {
-			return fmt.Errorf("failed to save config: %w", err)
+		// Remove the repo from config
+		if err := config.RemoveRepo(configPath, repoPath); err != nil {
+			return fmt.Errorf("failed to remove repository: %w", err)
 		}
 
 		if jsonOutput {
 			result := map[string]interface{}{
-				"removed": true,
-				"key":     key,
-				"path":    path,
+				"removed":        true,
+				"path":           repoPath,
+				"issues_deleted": deletedCount,
 			}
 			return json.NewEncoder(os.Stdout).Encode(result)
 		}
 
-		fmt.Printf("Removed repository: %s → %s\n", key, path)
+		fmt.Printf("Removed repository: %s\n", repoPath)
+		if deletedCount > 0 {
+			fmt.Printf("Deleted %d issue(s) from the database\n", deletedCount)
+		}
 		return nil
 	},
 }
@@ -121,32 +159,46 @@ var repoRemoveCmd = &cobra.Command{
 var repoListCmd = &cobra.Command{
 	Use:   "list",
 	Short: "List all configured repositories",
+	Long: `List all repositories configured in .beads/config.yaml.
+
+Shows the primary repository (always ".") and any additional
+repositories configured for hydration.`,
 	RunE: func(cmd *cobra.Command, args []string) error {
-		if err := ensureDirectMode("repo list requires direct database access"); err != nil {
-			return err
+		// Find config.yaml
+		configPath, err := config.FindConfigYAMLPath()
+		if err != nil {
+			return fmt.Errorf("failed to find config.yaml: %w", err)
 		}
 
-		ctx := rootCtx
-		repos, err := getRepoConfig(ctx, store)
+		// Get repos from YAML
+		repos, err := config.ListRepos(configPath)
 		if err != nil {
 			return fmt.Errorf("failed to load config: %w", err)
 		}
 
 		if jsonOutput {
+			primary := repos.Primary
+			if primary == "" {
+				primary = "."
+			}
 			result := map[string]interface{}{
-				"primary":    ".",
-				"additional": repos,
+				"primary":    primary,
+				"additional": repos.Additional,
 			}
 			return json.NewEncoder(os.Stdout).Encode(result)
 		}
 
-		fmt.Println("Primary repository: .")
-		if len(repos) == 0 {
+		primary := repos.Primary
+		if primary == "" {
+			primary = "."
+		}
+		fmt.Printf("Primary repository: %s\n", primary)
+		if len(repos.Additional) == 0 {
 			fmt.Println("No additional repositories configured")
 		} else {
 			fmt.Println("\nAdditional repositories:")
-			for key, path := range repos {
-				fmt.Printf("  %s → %s\n", key, path)
+			for _, path := range repos.Additional {
+				fmt.Printf("  - %s\n", path)
 			}
 		}
 		return nil
@@ -156,6 +208,10 @@ var repoListCmd = &cobra.Command{
 var repoSyncCmd = &cobra.Command{
 	Use:   "sync",
 	Short: "Manually trigger multi-repo sync",
+	Long: `Trigger synchronization from all configured repositories.
+
+This hydrates issues from all repos in repos.additional into the
+local database, then exports any local changes back to JSONL.`,
 	RunE: func(cmd *cobra.Command, args []string) error {
 		if err := ensureDirectMode("repo sync requires direct database access"); err != nil {
 			return err
@@ -186,39 +242,6 @@ var repoSyncCmd = &cobra.Command{
 	},
 }
 
-// Helper functions for repo config management
-func getRepoConfig(ctx context.Context, store storage.Storage) (map[string]string, error) {
-	value, err := store.GetConfig(ctx, "repos.additional")
-	if err != nil {
-		if strings.Contains(err.Error(), "not found") {
-			return make(map[string]string), nil
-		}
-		return nil, err
-	}
-
-	// Handle empty value (config key exists but no value set)
-	if value == "" {
-		return make(map[string]string), nil
-	}
-
-	// Parse JSON map
-	repos := make(map[string]string)
-	if err := json.Unmarshal([]byte(value), &repos); err != nil {
-		return nil, fmt.Errorf("failed to parse repos config: %w", err)
-	}
-
-	return repos, nil
-}
-
-func setRepoConfig(ctx context.Context, store storage.Storage, repos map[string]string) error {
-	data, err := json.Marshal(repos)
-	if err != nil {
-		return fmt.Errorf("failed to serialize repos: %w", err)
-	}
-
-	return store.SetConfig(ctx, "repos.additional", string(data))
-}
-
 func init() {
 	repoCmd.AddCommand(repoAddCmd)
 	repoCmd.AddCommand(repoRemoveCmd)

internal/config/repos.go

@@ -0,0 +1,269 @@
+package config
+
+import (
+	"fmt"
+	"os"
+	"path/filepath"
+	"strings"
+
+	"gopkg.in/yaml.v3"
+)
+
+// ReposConfig represents the repos section of config.yaml
+type ReposConfig struct {
+	Primary    string   `yaml:"primary,omitempty"`
+	Additional []string `yaml:"additional,omitempty,flow"`
+}
+
+// configFile represents the structure for reading/writing config.yaml
+// We use yaml.Node to preserve comments and formatting
+type configFile struct {
+	root yaml.Node
+}
+
+// FindConfigYAMLPath finds the config.yaml file in .beads directory
+// Walks up from CWD to find .beads/config.yaml
+func FindConfigYAMLPath() (string, error) {
+	cwd, err := os.Getwd()
+	if err != nil {
+		return "", fmt.Errorf("failed to get working directory: %w", err)
+	}
+
+	for dir := cwd; dir != filepath.Dir(dir); dir = filepath.Dir(dir) {
+		beadsDir := filepath.Join(dir, ".beads")
+		configPath := filepath.Join(beadsDir, "config.yaml")
+		if _, err := os.Stat(configPath); err == nil {
+			return configPath, nil
+		}
+	}
+
+	return "", fmt.Errorf("no .beads/config.yaml found in current directory or parents")
+}
+
+// GetReposFromYAML reads the repos configuration from config.yaml
+// Returns an empty ReposConfig if repos section doesn't exist
+func GetReposFromYAML(configPath string) (*ReposConfig, error) {
+	data, err := os.ReadFile(configPath) // #nosec G304 - config file path from caller
+	if err != nil {
+		if os.IsNotExist(err) {
+			return &ReposConfig{}, nil
+		}
+		return nil, fmt.Errorf("failed to read config.yaml: %w", err)
+	}
+
+	// Parse into a generic map to extract repos section
+	var cfg map[string]interface{}
+	if err := yaml.Unmarshal(data, &cfg); err != nil {
+		return nil, fmt.Errorf("failed to parse config.yaml: %w", err)
+	}
+
+	repos := &ReposConfig{}
+	if reposRaw, ok := cfg["repos"]; ok && reposRaw != nil {
+		reposMap, ok := reposRaw.(map[string]interface{})
+		if !ok {
+			return nil, fmt.Errorf("repos section is not a map")
+		}
+
+		if primary, ok := reposMap["primary"].(string); ok {
+			repos.Primary = primary
+		}
+
+		if additional, ok := reposMap["additional"]; ok && additional != nil {
+			switch v := additional.(type) {
+			case []interface{}:
+				for _, item := range v {
+					if str, ok := item.(string); ok {
+						repos.Additional = append(repos.Additional, str)
+					}
+				}
+			}
+		}
+	}
+
+	return repos, nil
+}
+
+// SetReposInYAML writes the repos configuration to config.yaml
+// It preserves other config sections and comments where possible
+func SetReposInYAML(configPath string, repos *ReposConfig) error {
+	// Read existing config or create new
+	data, err := os.ReadFile(configPath) // #nosec G304 - config file path from caller
+	if err != nil && !os.IsNotExist(err) {
+		return fmt.Errorf("failed to read config.yaml: %w", err)
+	}
+
+	// Parse existing config into yaml.Node to preserve structure
+	var root yaml.Node
+	if len(data) > 0 {
+		if err := yaml.Unmarshal(data, &root); err != nil {
+			return fmt.Errorf("failed to parse config.yaml: %w", err)
+		}
+	}
+
+	// Handle empty or comment-only files by creating a valid document structure
+	if root.Kind != yaml.DocumentNode || len(root.Content) == 0 {
+		root = yaml.Node{
+			Kind: yaml.DocumentNode,
+			Content: []*yaml.Node{
+				{Kind: yaml.MappingNode},
+			},
+		}
+	}
+
+	// Get the mapping node (first content of document)
+	mapping := root.Content[0]
+	if mapping.Kind != yaml.MappingNode {
+		// If the document content isn't a mapping, replace it with one
+		root.Content[0] = &yaml.Node{Kind: yaml.MappingNode}
+		mapping = root.Content[0]
+	}
+
+	// Find or create repos section
+	reposIndex := -1
+	for i := 0; i < len(mapping.Content); i += 2 {
+		if mapping.Content[i].Value == "repos" {
+			reposIndex = i
+			break
+		}
+	}
+
+	// Build the repos node
+	reposNode := buildReposNode(repos)
+
+	if reposIndex >= 0 {
+		// Update existing repos section
+		if reposNode == nil {
+			// Remove repos section entirely if empty
+			mapping.Content = append(mapping.Content[:reposIndex], mapping.Content[reposIndex+2:]...)
+		} else {
+			mapping.Content[reposIndex+1] = reposNode
+		}
+	} else if reposNode != nil {
+		// Add new repos section at the end
+		mapping.Content = append(mapping.Content,
+			&yaml.Node{Kind: yaml.ScalarNode, Value: "repos"},
+			reposNode,
+		)
+	}
+
+	// Marshal back to YAML
+	var buf strings.Builder
+	encoder := yaml.NewEncoder(&buf)
+	encoder.SetIndent(2)
+	if err := encoder.Encode(&root); err != nil {
+		return fmt.Errorf("failed to encode config.yaml: %w", err)
+	}
+	if err := encoder.Close(); err != nil {
+		return fmt.Errorf("failed to close encoder: %w", err)
+	}
+
+	// Write back to file
+	if err := os.WriteFile(configPath, []byte(buf.String()), 0600); err != nil {
+		return fmt.Errorf("failed to write config.yaml: %w", err)
+	}
+
+	// Reload viper config so changes take effect immediately
+	if v != nil {
+		if err := v.ReadInConfig(); err != nil {
+			// Not fatal - config is on disk, will be picked up on next command
+			_ = err
+		}
+	}
+
+	return nil
+}
+
+// buildReposNode creates a yaml.Node for the repos configuration
+// Returns nil if repos is empty (no primary and no additional)
+func buildReposNode(repos *ReposConfig) *yaml.Node {
+	if repos == nil || (repos.Primary == "" && len(repos.Additional) == 0) {
+		return nil
+	}
+
+	node := &yaml.Node{Kind: yaml.MappingNode}
+
+	if repos.Primary != "" {
+		node.Content = append(node.Content,
+			&yaml.Node{Kind: yaml.ScalarNode, Value: "primary"},
+			&yaml.Node{Kind: yaml.ScalarNode, Value: repos.Primary, Style: yaml.DoubleQuotedStyle},
+		)
+	}
+
+	if len(repos.Additional) > 0 {
+		additionalNode := &yaml.Node{Kind: yaml.SequenceNode}
+		for _, path := range repos.Additional {
+			additionalNode.Content = append(additionalNode.Content,
+				&yaml.Node{Kind: yaml.ScalarNode, Value: path, Style: yaml.DoubleQuotedStyle},
+			)
+		}
+		node.Content = append(node.Content,
+			&yaml.Node{Kind: yaml.ScalarNode, Value: "additional"},
+			additionalNode,
+		)
+	}
+
+	return node
+}
+
+// AddRepo adds a repository to the repos.additional list in config.yaml
+// If primary is not set, it defaults to "."
+func AddRepo(configPath, repoPath string) error {
+	repos, err := GetReposFromYAML(configPath)
+	if err != nil {
+		return fmt.Errorf("failed to get repos config: %w", err)
+	}
+
+	// Set primary to "." if not already set (standard multi-repo convention)
+	if repos.Primary == "" {
+		repos.Primary = "."
+	}
+
+	// Check if repo already exists
+	for _, existing := range repos.Additional {
+		if existing == repoPath {
+			return fmt.Errorf("repository already configured: %s", repoPath)
+		}
+	}
+
+	// Add the new repo
+	repos.Additional = append(repos.Additional, repoPath)
+
+	return SetReposInYAML(configPath, repos)
+}
+
+// RemoveRepo removes a repository from the repos.additional list in config.yaml
+func RemoveRepo(configPath, repoPath string) error {
+	repos, err := GetReposFromYAML(configPath)
+	if err != nil {
+		return fmt.Errorf("failed to get repos config: %w", err)
+	}
+
+	// Find and remove the repo
+	found := false
+	newAdditional := make([]string, 0, len(repos.Additional))
+	for _, existing := range repos.Additional {
+		if existing == repoPath {
+			found = true
+			continue
+		}
+		newAdditional = append(newAdditional, existing)
+	}
+
+	if !found {
+		return fmt.Errorf("repository not found: %s", repoPath)
+	}
+
+	repos.Additional = newAdditional
+
+	// If no repos left, clear primary too
+	if len(repos.Additional) == 0 {
+		repos.Primary = ""
+	}
+
+	return SetReposInYAML(configPath, repos)
+}
+
+// ListRepos returns the current repos configuration from YAML
+func ListRepos(configPath string) (*ReposConfig, error) {
+	return GetReposFromYAML(configPath)
+}

internal/config/repos_test.go

@@ -0,0 +1,286 @@
+package config
+
+import (
+	"os"
+	"path/filepath"
+	"testing"
+)
+
+func TestGetReposFromYAML_Empty(t *testing.T) {
+	// Create temp dir with empty config.yaml
+	tmpDir := t.TempDir()
+	configPath := filepath.Join(tmpDir, "config.yaml")
+	if err := os.WriteFile(configPath, []byte("# empty config\n"), 0600); err != nil {
+		t.Fatal(err)
+	}
+
+	repos, err := GetReposFromYAML(configPath)
+	if err != nil {
+		t.Fatalf("GetReposFromYAML failed: %v", err)
+	}
+
+	if repos.Primary != "" {
+		t.Errorf("expected empty primary, got %q", repos.Primary)
+	}
+	if len(repos.Additional) != 0 {
+		t.Errorf("expected empty additional, got %v", repos.Additional)
+	}
+}
+
+func TestGetReposFromYAML_WithRepos(t *testing.T) {
+	tmpDir := t.TempDir()
+	configPath := filepath.Join(tmpDir, "config.yaml")
+	config := `repos:
+  primary: "."
+  additional:
+    - ~/beads-planning
+    - /path/to/other
+`
+	if err := os.WriteFile(configPath, []byte(config), 0600); err != nil {
+		t.Fatal(err)
+	}
+
+	repos, err := GetReposFromYAML(configPath)
+	if err != nil {
+		t.Fatalf("GetReposFromYAML failed: %v", err)
+	}
+
+	if repos.Primary != "." {
+		t.Errorf("expected primary='.', got %q", repos.Primary)
+	}
+	if len(repos.Additional) != 2 {
+		t.Fatalf("expected 2 additional repos, got %d", len(repos.Additional))
+	}
+	if repos.Additional[0] != "~/beads-planning" {
+		t.Errorf("expected first additional='~/beads-planning', got %q", repos.Additional[0])
+	}
+	if repos.Additional[1] != "/path/to/other" {
+		t.Errorf("expected second additional='/path/to/other', got %q", repos.Additional[1])
+	}
+}
+
+func TestSetReposInYAML_NewFile(t *testing.T) {
+	tmpDir := t.TempDir()
+	configPath := filepath.Join(tmpDir, "config.yaml")
+
+	repos := &ReposConfig{
+		Primary:    ".",
+		Additional: []string{"~/test-repo"},
+	}
+
+	if err := SetReposInYAML(configPath, repos); err != nil {
+		t.Fatalf("SetReposInYAML failed: %v", err)
+	}
+
+	// Verify by reading back
+	readRepos, err := GetReposFromYAML(configPath)
+	if err != nil {
+		t.Fatalf("GetReposFromYAML failed: %v", err)
+	}
+
+	if readRepos.Primary != "." {
+		t.Errorf("expected primary='.', got %q", readRepos.Primary)
+	}
+	if len(readRepos.Additional) != 1 || readRepos.Additional[0] != "~/test-repo" {
+		t.Errorf("expected additional=['~/test-repo'], got %v", readRepos.Additional)
+	}
+}
+
+func TestSetReposInYAML_PreservesOtherConfig(t *testing.T) {
+	tmpDir := t.TempDir()
+	configPath := filepath.Join(tmpDir, "config.yaml")
+
+	// Write initial config with other settings
+	initial := `issue-prefix: "test"
+sync-branch: "beads-sync"
+json: false
+`
+	if err := os.WriteFile(configPath, []byte(initial), 0600); err != nil {
+		t.Fatal(err)
+	}
+
+	// Add repos
+	repos := &ReposConfig{
+		Primary:    ".",
+		Additional: []string{"~/test-repo"},
+	}
+	if err := SetReposInYAML(configPath, repos); err != nil {
+		t.Fatalf("SetReposInYAML failed: %v", err)
+	}
+
+	// Verify content still has other settings
+	data, err := os.ReadFile(configPath)
+	if err != nil {
+		t.Fatal(err)
+	}
+	content := string(data)
+
+	// Check that original settings are preserved
+	if !contains(content, "issue-prefix") {
+		t.Error("issue-prefix setting was lost")
+	}
+	if !contains(content, "sync-branch") {
+		t.Error("sync-branch setting was lost")
+	}
+	if !contains(content, "json") {
+		t.Error("json setting was lost")
+	}
+
+	// Check that repos section was added
+	if !contains(content, "repos:") {
+		t.Error("repos section not found")
+	}
+}
+
+func TestAddRepo(t *testing.T) {
+	tmpDir := t.TempDir()
+	configPath := filepath.Join(tmpDir, "config.yaml")
+	if err := os.WriteFile(configPath, []byte("# config\n"), 0600); err != nil {
+		t.Fatal(err)
+	}
+
+	// Add first repo
+	if err := AddRepo(configPath, "~/first-repo"); err != nil {
+		t.Fatalf("AddRepo failed: %v", err)
+	}
+
+	repos, err := GetReposFromYAML(configPath)
+	if err != nil {
+		t.Fatal(err)
+	}
+	if repos.Primary != "." {
+		t.Errorf("expected primary='.', got %q", repos.Primary)
+	}
+	if len(repos.Additional) != 1 || repos.Additional[0] != "~/first-repo" {
+		t.Errorf("unexpected additional: %v", repos.Additional)
+	}
+
+	// Add second repo
+	if err := AddRepo(configPath, "/path/to/second"); err != nil {
+		t.Fatalf("AddRepo failed: %v", err)
+	}
+
+	repos, err = GetReposFromYAML(configPath)
+	if err != nil {
+		t.Fatal(err)
+	}
+	if len(repos.Additional) != 2 {
+		t.Fatalf("expected 2 additional repos, got %d", len(repos.Additional))
+	}
+}
+
+func TestAddRepo_Duplicate(t *testing.T) {
+	tmpDir := t.TempDir()
+	configPath := filepath.Join(tmpDir, "config.yaml")
+	if err := os.WriteFile(configPath, []byte("# config\n"), 0600); err != nil {
+		t.Fatal(err)
+	}
+
+	// Add repo
+	if err := AddRepo(configPath, "~/test-repo"); err != nil {
+		t.Fatalf("AddRepo failed: %v", err)
+	}
+
+	// Try to add same repo again - should fail
+	err := AddRepo(configPath, "~/test-repo")
+	if err == nil {
+		t.Error("expected error for duplicate repo, got nil")
+	}
+}
+
+func TestRemoveRepo(t *testing.T) {
+	tmpDir := t.TempDir()
+	configPath := filepath.Join(tmpDir, "config.yaml")
+	config := `repos:
+  primary: "."
+  additional:
+    - ~/first
+    - ~/second
+`
+	if err := os.WriteFile(configPath, []byte(config), 0600); err != nil {
+		t.Fatal(err)
+	}
+
+	// Remove first repo
+	if err := RemoveRepo(configPath, "~/first"); err != nil {
+		t.Fatalf("RemoveRepo failed: %v", err)
+	}
+
+	repos, err := GetReposFromYAML(configPath)
+	if err != nil {
+		t.Fatal(err)
+	}
+	if len(repos.Additional) != 1 || repos.Additional[0] != "~/second" {
+		t.Errorf("unexpected additional after remove: %v", repos.Additional)
+	}
+
+	// Remove last repo - should clear primary too
+	if err := RemoveRepo(configPath, "~/second"); err != nil {
+		t.Fatalf("RemoveRepo failed: %v", err)
+	}
+
+	repos, err = GetReposFromYAML(configPath)
+	if err != nil {
+		t.Fatal(err)
+	}
+	if repos.Primary != "" {
+		t.Errorf("expected empty primary after removing all repos, got %q", repos.Primary)
+	}
+	if len(repos.Additional) != 0 {
+		t.Errorf("expected empty additional after removing all repos, got %v", repos.Additional)
+	}
+}
+
+func TestRemoveRepo_NotFound(t *testing.T) {
+	tmpDir := t.TempDir()
+	configPath := filepath.Join(tmpDir, "config.yaml")
+	if err := os.WriteFile(configPath, []byte("# config\n"), 0600); err != nil {
+		t.Fatal(err)
+	}
+
+	err := RemoveRepo(configPath, "~/nonexistent")
+	if err == nil {
+		t.Error("expected error for nonexistent repo, got nil")
+	}
+}
+
+func TestFindConfigYAMLPath(t *testing.T) {
+	// Create temp dir with .beads/config.yaml
+	tmpDir := t.TempDir()
+	beadsDir := filepath.Join(tmpDir, ".beads")
+	if err := os.MkdirAll(beadsDir, 0755); err != nil {
+		t.Fatal(err)
+	}
+	configPath := filepath.Join(beadsDir, "config.yaml")
+	if err := os.WriteFile(configPath, []byte("# config\n"), 0600); err != nil {
+		t.Fatal(err)
+	}
+
+	// Change to the temp dir
+	oldWd, _ := os.Getwd()
+	defer func() {
+		if err := os.Chdir(oldWd); err != nil {
+			t.Logf("warning: failed to restore working directory: %v", err)
+		}
+	}()
+	if err := os.Chdir(tmpDir); err != nil {
+		t.Fatal(err)
+	}
+
+	found, err := FindConfigYAMLPath()
+	if err != nil {
+		t.Fatalf("FindConfigYAMLPath failed: %v", err)
+	}
+
+	// Verify path ends with .beads/config.yaml
+	if filepath.Base(found) != "config.yaml" {
+		t.Errorf("expected path ending with config.yaml, got %s", found)
+	}
+	if filepath.Base(filepath.Dir(found)) != ".beads" {
+		t.Errorf("expected path in .beads dir, got %s", found)
+	}
+}
+
+func contains(s, substr string) bool {
+	return len(s) >= len(substr) && (s == substr || len(s) > 0 && (s[0:len(substr)] == substr || contains(s[1:], substr)))
+}

internal/storage/sqlite/multirepo.go

@@ -388,6 +388,124 @@ func (s *SQLiteStorage) upsertIssueInTx(ctx context.Context, tx *sql.Tx, issue *
 	return nil
 }
 
+// DeleteIssuesBySourceRepo permanently removes all issues from a specific source repository.
+// This is used when a repo is removed from the multi-repo configuration.
+// It also cleans up related data: dependencies, labels, comments, events, and dirty markers.
+// Returns the number of issues deleted.
+func (s *SQLiteStorage) DeleteIssuesBySourceRepo(ctx context.Context, sourceRepo string) (int, error) {
+	tx, err := s.db.BeginTx(ctx, nil)
+	if err != nil {
+		return 0, fmt.Errorf("failed to begin transaction: %w", err)
+	}
+	defer func() { _ = tx.Rollback() }()
+
+	// Get the list of issue IDs to delete
+	rows, err := tx.QueryContext(ctx, `SELECT id FROM issues WHERE source_repo = ?`, sourceRepo)
+	if err != nil {
+		return 0, fmt.Errorf("failed to query issues: %w", err)
+	}
+	var issueIDs []string
+	for rows.Next() {
+		var id string
+		if err := rows.Scan(&id); err != nil {
+			rows.Close()
+			return 0, fmt.Errorf("failed to scan issue ID: %w", err)
+		}
+		issueIDs = append(issueIDs, id)
+	}
+	rows.Close()
+	if err := rows.Err(); err != nil {
+		return 0, fmt.Errorf("failed to iterate issues: %w", err)
+	}
+
+	if len(issueIDs) == 0 {
+		if err := tx.Commit(); err != nil {
+			return 0, fmt.Errorf("failed to commit empty transaction: %w", err)
+		}
+		return 0, nil
+	}
+
+	// Delete dependencies (both directions) for all affected issues
+	for _, id := range issueIDs {
+		_, err = tx.ExecContext(ctx, `DELETE FROM dependencies WHERE issue_id = ? OR depends_on_id = ?`, id, id)
+		if err != nil {
+			return 0, fmt.Errorf("failed to delete dependencies for %s: %w", id, err)
+		}
+	}
+
+	// Delete events for all affected issues
+	for _, id := range issueIDs {
+		_, err = tx.ExecContext(ctx, `DELETE FROM events WHERE issue_id = ?`, id)
+		if err != nil {
+			return 0, fmt.Errorf("failed to delete events for %s: %w", id, err)
+		}
+	}
+
+	// Delete comments for all affected issues
+	for _, id := range issueIDs {
+		_, err = tx.ExecContext(ctx, `DELETE FROM comments WHERE issue_id = ?`, id)
+		if err != nil {
+			return 0, fmt.Errorf("failed to delete comments for %s: %w", id, err)
+		}
+	}
+
+	// Delete labels for all affected issues
+	for _, id := range issueIDs {
+		_, err = tx.ExecContext(ctx, `DELETE FROM labels WHERE issue_id = ?`, id)
+		if err != nil {
+			return 0, fmt.Errorf("failed to delete labels for %s: %w", id, err)
+		}
+	}
+
+	// Delete dirty markers for all affected issues
+	for _, id := range issueIDs {
+		_, err = tx.ExecContext(ctx, `DELETE FROM dirty_issues WHERE issue_id = ?`, id)
+		if err != nil {
+			return 0, fmt.Errorf("failed to delete dirty marker for %s: %w", id, err)
+		}
+	}
+
+	// Delete the issues themselves
+	result, err := tx.ExecContext(ctx, `DELETE FROM issues WHERE source_repo = ?`, sourceRepo)
+	if err != nil {
+		return 0, fmt.Errorf("failed to delete issues: %w", err)
+	}
+
+	rowsAffected, err := result.RowsAffected()
+	if err != nil {
+		return 0, fmt.Errorf("failed to check rows affected: %w", err)
+	}
+
+	if err := tx.Commit(); err != nil {
+		return 0, fmt.Errorf("failed to commit transaction: %w", err)
+	}
+
+	return int(rowsAffected), nil
+}
+
+// ClearRepoMtime removes the mtime cache entry for a repository.
+// This is used when a repo is removed from the multi-repo configuration.
+func (s *SQLiteStorage) ClearRepoMtime(ctx context.Context, repoPath string) error {
+	// Expand tilde in path to match how it's stored
+	expandedPath, err := expandTilde(repoPath)
+	if err != nil {
+		return fmt.Errorf("failed to expand path: %w", err)
+	}
+
+	// Get absolute path to match how it's stored in repo_mtimes
+	absRepoPath, err := filepath.Abs(expandedPath)
+	if err != nil {
+		return fmt.Errorf("failed to get absolute path: %w", err)
+	}
+
+	_, err = s.db.ExecContext(ctx, `DELETE FROM repo_mtimes WHERE repo_path = ?`, absRepoPath)
+	if err != nil {
+		return fmt.Errorf("failed to delete mtime cache: %w", err)
+	}
+
+	return nil
+}
+
 // expandTilde expands ~ in a file path to the user's home directory.
 func expandTilde(path string) (string, error) {
 	if !strings.HasPrefix(path, "~") {

internal/storage/sqlite/multirepo_test.go

@@ -500,6 +500,263 @@ func TestImportJSONLFileOutOfOrderDeps(t *testing.T) {
 	})
 }
 
+func TestDeleteIssuesBySourceRepo(t *testing.T) {
+	t.Run("deletes all issues from specified repo", func(t *testing.T) {
+		store, cleanup := setupTestDB(t)
+		defer cleanup()
+
+		ctx := context.Background()
+
+		// Create issues with different source_repos
+		issue1 := &types.Issue{
+			ID:         "bd-repo1-1",
+			Title:      "Repo1 Issue 1",
+			Status:     types.StatusOpen,
+			Priority:   1,
+			IssueType:  types.TypeTask,
+			CreatedAt:  time.Now(),
+			UpdatedAt:  time.Now(),
+			SourceRepo: "~/test-repo",
+		}
+		issue1.ContentHash = issue1.ComputeContentHash()
+
+		issue2 := &types.Issue{
+			ID:         "bd-repo1-2",
+			Title:      "Repo1 Issue 2",
+			Status:     types.StatusOpen,
+			Priority:   1,
+			IssueType:  types.TypeTask,
+			CreatedAt:  time.Now(),
+			UpdatedAt:  time.Now(),
+			SourceRepo: "~/test-repo",
+		}
+		issue2.ContentHash = issue2.ComputeContentHash()
+
+		issue3 := &types.Issue{
+			ID:         "bd-primary-1",
+			Title:      "Primary Issue",
+			Status:     types.StatusOpen,
+			Priority:   1,
+			IssueType:  types.TypeTask,
+			CreatedAt:  time.Now(),
+			UpdatedAt:  time.Now(),
+			SourceRepo: ".",
+		}
+		issue3.ContentHash = issue3.ComputeContentHash()
+
+		// Insert all issues
+		if err := store.CreateIssue(ctx, issue1, "test"); err != nil {
+			t.Fatalf("failed to create issue1: %v", err)
+		}
+		if err := store.CreateIssue(ctx, issue2, "test"); err != nil {
+			t.Fatalf("failed to create issue2: %v", err)
+		}
+		if err := store.CreateIssue(ctx, issue3, "test"); err != nil {
+			t.Fatalf("failed to create issue3: %v", err)
+		}
+
+		// Delete issues from ~/test-repo
+		deletedCount, err := store.DeleteIssuesBySourceRepo(ctx, "~/test-repo")
+		if err != nil {
+			t.Fatalf("DeleteIssuesBySourceRepo() error = %v", err)
+		}
+		if deletedCount != 2 {
+			t.Errorf("expected 2 issues deleted, got %d", deletedCount)
+		}
+
+		// Verify ~/test-repo issues are gone
+		// GetIssue returns (nil, nil) when issue doesn't exist
+		issue1After, err := store.GetIssue(ctx, "bd-repo1-1")
+		if issue1After != nil || err != nil {
+			t.Errorf("expected bd-repo1-1 to be deleted, got issue=%v, err=%v", issue1After, err)
+		}
+		issue2After, err := store.GetIssue(ctx, "bd-repo1-2")
+		if issue2After != nil || err != nil {
+			t.Errorf("expected bd-repo1-2 to be deleted, got issue=%v, err=%v", issue2After, err)
+		}
+
+		// Verify primary issue still exists
+		primary, err := store.GetIssue(ctx, "bd-primary-1")
+		if err != nil {
+			t.Fatalf("primary issue should still exist: %v", err)
+		}
+		if primary.Title != "Primary Issue" {
+			t.Errorf("expected 'Primary Issue', got %q", primary.Title)
+		}
+	})
+
+	t.Run("returns 0 when no issues match", func(t *testing.T) {
+		store, cleanup := setupTestDB(t)
+		defer cleanup()
+
+		ctx := context.Background()
+
+		// Create an issue with a different source_repo
+		issue := &types.Issue{
+			ID:         "bd-other-1",
+			Title:      "Other Issue",
+			Status:     types.StatusOpen,
+			Priority:   1,
+			IssueType:  types.TypeTask,
+			CreatedAt:  time.Now(),
+			UpdatedAt:  time.Now(),
+			SourceRepo: ".",
+		}
+		issue.ContentHash = issue.ComputeContentHash()
+
+		if err := store.CreateIssue(ctx, issue, "test"); err != nil {
+			t.Fatalf("failed to create issue: %v", err)
+		}
+
+		// Delete from non-existent repo
+		deletedCount, err := store.DeleteIssuesBySourceRepo(ctx, "~/nonexistent")
+		if err != nil {
+			t.Fatalf("DeleteIssuesBySourceRepo() error = %v", err)
+		}
+		if deletedCount != 0 {
+			t.Errorf("expected 0 issues deleted, got %d", deletedCount)
+		}
+
+		// Verify original issue still exists
+		_, err = store.GetIssue(ctx, "bd-other-1")
+		if err != nil {
+			t.Errorf("issue should still exist: %v", err)
+		}
+	})
+
+	t.Run("cleans up related data", func(t *testing.T) {
+		store, cleanup := setupTestDB(t)
+		defer cleanup()
+
+		ctx := context.Background()
+
+		// Create an issue with labels and comments
+		issue := &types.Issue{
+			ID:         "bd-cleanup-1",
+			Title:      "Cleanup Test Issue",
+			Status:     types.StatusOpen,
+			Priority:   1,
+			IssueType:  types.TypeTask,
+			CreatedAt:  time.Now(),
+			UpdatedAt:  time.Now(),
+			SourceRepo: "~/cleanup-repo",
+			Labels:     []string{"test", "cleanup"},
+		}
+		issue.ContentHash = issue.ComputeContentHash()
+
+		if err := store.CreateIssue(ctx, issue, "test"); err != nil {
+			t.Fatalf("failed to create issue: %v", err)
+		}
+
+		// Add a comment
+		_, err := store.AddIssueComment(ctx, "bd-cleanup-1", "test", "Test comment")
+		if err != nil {
+			t.Fatalf("failed to add comment: %v", err)
+		}
+
+		// Delete the repo
+		deletedCount, err := store.DeleteIssuesBySourceRepo(ctx, "~/cleanup-repo")
+		if err != nil {
+			t.Fatalf("DeleteIssuesBySourceRepo() error = %v", err)
+		}
+		if deletedCount != 1 {
+			t.Errorf("expected 1 issue deleted, got %d", deletedCount)
+		}
+
+		// Verify issue is gone
+		// GetIssue returns (nil, nil) when issue doesn't exist
+		issueAfter, err := store.GetIssue(ctx, "bd-cleanup-1")
+		if issueAfter != nil || err != nil {
+			t.Errorf("expected issue to be deleted, got issue=%v, err=%v", issueAfter, err)
+		}
+
+		// Verify labels are gone (query directly to check)
+		var labelCount int
+		err = store.db.QueryRowContext(ctx, `SELECT COUNT(*) FROM labels WHERE issue_id = ?`, "bd-cleanup-1").Scan(&labelCount)
+		if err != nil {
+			t.Fatalf("failed to query labels: %v", err)
+		}
+		if labelCount != 0 {
+			t.Errorf("expected 0 labels, got %d", labelCount)
+		}
+
+		// Verify comments are gone
+		var commentCount int
+		err = store.db.QueryRowContext(ctx, `SELECT COUNT(*) FROM comments WHERE issue_id = ?`, "bd-cleanup-1").Scan(&commentCount)
+		if err != nil {
+			t.Fatalf("failed to query comments: %v", err)
+		}
+		if commentCount != 0 {
+			t.Errorf("expected 0 comments, got %d", commentCount)
+		}
+	})
+}
+
+func TestClearRepoMtime(t *testing.T) {
+	t.Run("clears mtime cache for repo", func(t *testing.T) {
+		store, cleanup := setupTestDB(t)
+		defer cleanup()
+
+		ctx := context.Background()
+
+		// Insert a mtime cache entry directly
+		tmpDir := t.TempDir()
+		jsonlPath := filepath.Join(tmpDir, "issues.jsonl")
+
+		// Create a dummy JSONL file for the mtime
+		f, err := os.Create(jsonlPath)
+		if err != nil {
+			t.Fatalf("failed to create JSONL: %v", err)
+		}
+		f.Close()
+
+		_, err = store.db.ExecContext(ctx, `
+			INSERT INTO repo_mtimes (repo_path, jsonl_path, mtime_ns, last_checked)
+			VALUES (?, ?, ?, ?)
+		`, tmpDir, jsonlPath, 12345, time.Now())
+		if err != nil {
+			t.Fatalf("failed to insert mtime cache: %v", err)
+		}
+
+		// Verify it exists
+		var count int
+		err = store.db.QueryRowContext(ctx, `SELECT COUNT(*) FROM repo_mtimes WHERE repo_path = ?`, tmpDir).Scan(&count)
+		if err != nil {
+			t.Fatalf("failed to query mtime cache: %v", err)
+		}
+		if count != 1 {
+			t.Fatalf("expected 1 mtime cache entry, got %d", count)
+		}
+
+		// Clear it
+		if err := store.ClearRepoMtime(ctx, tmpDir); err != nil {
+			t.Fatalf("ClearRepoMtime() error = %v", err)
+		}
+
+		// Verify it's gone
+		err = store.db.QueryRowContext(ctx, `SELECT COUNT(*) FROM repo_mtimes WHERE repo_path = ?`, tmpDir).Scan(&count)
+		if err != nil {
+			t.Fatalf("failed to query mtime cache: %v", err)
+		}
+		if count != 0 {
+			t.Errorf("expected 0 mtime cache entries, got %d", count)
+		}
+	})
+
+	t.Run("handles non-existent repo gracefully", func(t *testing.T) {
+		store, cleanup := setupTestDB(t)
+		defer cleanup()
+
+		ctx := context.Background()
+
+		// Clear a repo that doesn't exist in cache - should not error
+		err := store.ClearRepoMtime(ctx, "/nonexistent/path")
+		if err != nil {
+			t.Errorf("ClearRepoMtime() should not error for non-existent path: %v", err)
+		}
+	})
+}
+
 func TestExportToMultiRepo(t *testing.T) {
 	t.Run("returns nil in single-repo mode", func(t *testing.T) {
 		store, cleanup := setupTestDB(t)